Re: [ccp4bb] Nitrate versus Carbonate

Yes, exactly, those two proteins. Were you involved? JPK From: Clement Angkawidjaja [mailto:clem...@evec.jp] Sent: Monday, November 14, 2016 12:42 AM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Nitrate versus Carbonate Maybe the Ca i

Re: [ccp4bb] Nitrate versus Carbonate

Maybe the Ca is just there as an additional binding site for carbonate. Btw, are you looking at CmpA/NrtA? Cheers, Clement From: Keller, Jacob Sent: Friday, November 11, 2016 2:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Nitrate versus Carbonate Well, I was looking at two

Re: [ccp4bb] Nitrate versus Carbonate

Once again, chemical intuition may help. At neutral pH values, sulfate is going to be present at SO4(2-), whereas phosphate will be present as H2PO4(-) or HPO4(2-). The hydrogen bond network supporting binding may be able to offer clues. Sulfate is not likely to have any H-bond acceptors in

Re: [ccp4bb] Nitrate versus Carbonate

Assuming it wasn't clear from purification/crystallisation reagents... Maybe try a high multiplicity anomalous dataset collected in house / at long wavelength? P has ~ 75% the f" of S at CuKa. If you can figure out roughly what anomalous peak height an S atom gives from a Cys or a Met with

Re: [ccp4bb] Nitrate versus Carbonate

Similarly, how do you differentiate a phosphate ion than sulfate just based on electron density if data is not at atomic resolution? Thanks! On Fri, Nov 11, 2016 at 3:52 AM, Harry Powell wrote: > Hi all > > Sticking to the first question, if you don't restrict

Re: [ccp4bb] Nitrate versus Carbonate

Hi all Sticking to the first question, if you don't restrict yourself to _X-ray_ crystallography but use your local neutron source instead, it should be straightforward (subject to all the normal caveats). On 10 Nov 2016, at 23:02, Tim Gruene wrote: > Dear JPK, > > to answer your first

Re: [ccp4bb] Nitrate versus Carbonate

, Jacob<mailto:kell...@janelia.hhmi.org> Sent: Friday, November 11, 2016 5:41 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Nitrate versus Carbonate Dear Crystallographers, I don’t think there is any feasible way crystallographically to distinguish bet

Re: [ccp4bb] Nitrate versus Carbonate

Sent: Friday, November 11, 2016 5:41 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Nitrate versus Carbonate Dear Crystallographers, I don’t think there is any feasible way crystallographically to distinguish between nitrate and carbonate or bicarbonate—correct? But that is not my main

Re: [ccp4bb] Nitrate versus Carbonate

Bicarbonate ion is a weak base and is normally protonated near neutral pH. (Nitrate is a pathetically weak base and is not protonated at any reasonable biological pH.) Therefore, bicarbonate will have one hydrogen bond donor group (the -OH group) and two hydrogen bond acceptor groups, whereas

Re: [ccp4bb] Nitrate versus Carbonate

Dear JPK, to answer your first question, at atomic resolution you would notice a density difference between N and C. At a little less resolution you might still measure difference in bond length. Regrds, Tim On Thursday, November 10, 2016 8:41:43 PM CET Keller, Jacob wrote: > Dear

Re: [ccp4bb] Nitrate versus Carbonate

Of Keller, Jacob Sent: Thursday, November 10, 2016 3:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Nitrate versus Carbonate Dear Crystallographers, I don't think there is any feasible way crystallographically to distinguish between nitrate and carbonate or bicarbonate-correct? But that is not my

Re: [ccp4bb] Nitrate versus Carbonate

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Nitrate versus Carbonate If I had to speculate, the polarity vector vs. atomic geometry would be the difference to utilize. The pKa of carbonate is around 6.3 for the first oxygen, so at physiological pH I would assume the majority of carbonate

[ccp4bb] Nitrate versus Carbonate

Dear Crystallographers, I don't think there is any feasible way crystallographically to distinguish between nitrate and carbonate or bicarbonate-correct? But that is not my main question. My main question is: given that nitrate and carbonate are both very important and also very different